microbiome-os DomainOS¶
Status: Graduated (production, ADR-009)
Engine: microbiome-os
Domain: Microbial communities (16S, metagenomics, amplicon, resistome)
Metagenomics DomainOS: 16S/ITS amplicon analysis, shotgun metagenomics, resistome profiling, and QIIME pipelines. Graduated 2026-04-12 (ADR-009) with ~23 skills and 517 passing tests; 5-artifact compliance is Wave 3C debt.
| Field | Value |
|---|---|
| Product | microbiome-os |
| Engine id | microbiome-os |
| Intent key | microbiome_os |
| Repository | Hordago-Labs/microbiome-os |
| Plugin | microbiome-os |
| Maturity (registry) | Graduated (production, ADR-009) |
Overview¶
Metagenomics DomainOS: 16S/ITS amplicon analysis, shotgun metagenomics, resistome profiling, and QIIME pipelines. Graduated 2026-04-12 (ADR-009) with ~23 skills and 517 passing tests; 5-artifact compliance is Wave 3C debt.
Scientific approach¶
microbiome-os structures every run as 5 phases. Gates marked HITL require an explicit human-in-the-loop approval before the run advances.
| # | Phase | Gate | HITL |
|---|---|---|---|
| 1 | Demux & QC | Demultiplex reads and run quality control. | No |
| 2 | Feature Inference | Infer ASVs/OTUs (QIIME/DADA2). | No |
| 3 | Taxonomic Assignment | Assign taxonomy. | No |
| 4 | Community Analysis | Compute diversity and differential abundance. | No |
| 5 | Resistome Profiling | Profile antimicrobial resistance genes. | Yes |
Capabilities & evidence objects¶
Domain tools / skills
amplicon-dada2shotgun-metagenomicsresistome-profilingqiime-pipeline
Evidence objects
| Object | Role | Consumer |
|---|---|---|
result.json |
produces | co-writer |
provenance.json |
produces | evidence-audit |
Canonical artifacts (5-artifact contract)
Planned
The 5-artifact contract below is the target shape. Canonical-artifact emission is tracked as inherited debt (Wave 3C) and is not yet guaranteed.
| Artifact | Description |
|---|---|
result.json |
Structured primary result payload for the domain run. |
report.md |
Human-readable narrative summary of the analysis. |
provenance.json |
Tool versions, reference data, and algorithm lineage for reproducibility. |
gate_status.json |
Per-phase gate pass/fail decisions. |
session_summary.json |
Session metadata for replay and audit. |
Standalone quickstart¶
Zero platform dependency
This quickstart runs the DomainOS standalone. The Hordago platform is not required; platform composition is opt-in (see Composition below).
- Install the standalone
microbiome-osplugin (Hordago-Labs/microbiome-os) -- no Hordago platform required. - Invoke the domain skill with a microbiome-os intent (see the intent keywords below).
- Review the emitted artifacts under the run's output directory.
Intent keywords (route to this engine):
microbiome \b16s\b metagenomics amplicon resistome qiime metagenomic gut flora microbial community
Worked example¶
16S amplicon community analysis
A user provides 16S amplicon reads. microbiome-os demultiplexes, runs DADA2 to infer ASVs, assigns taxonomy, computes alpha/beta diversity and differential abundance, then profiles the resistome.
Validation & benchmarks¶
Benchmarks
- Mock-community composition recovery
- Diversity-metric regression
Reproducibility. provenance.json pins reference database version and QIIME plugin versions.
Reference¶
MCP fallback servers (used when the plugin is unavailable): pubmed
Source documents
- Scaffold-domains ledger (microbiome-os):
references/scaffold-domains.md
Composition¶
Platform opt-in
microbiome-os runs standalone. When composed under the Hordago platform it gains cross-domain routing, the Shared Compiler gate, and evidence-audit provenance enforcement. Platform composition is opt-in; the quickstart above has zero platform dependency.
Cross-domain dependencies
| Engine | Relationship |
|---|---|
bioinformatics-os |
Uses the Shared Compiler gate for experiment designs. |